chr15-33212866-C-A

Variant names:

• chr15-33212866-C-A
• rs974379
• ENST00000796872.1:n.639C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000796872.1(ENSG00000289896):​n.639C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 151,958 control chromosomes in the GnomAD database, including 49,714 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (49714 hom., cov: 31)
• Consequence: ENSG00000289896 ENST00000796872.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 6 publications found

Genes affected

ENSG00000289896 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289896	ENST00000796872.1	n.639C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118026 AN: 151840 Hom.: 49706 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.796

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.777 AC: 118069 AN: 151958 Hom.: 49714 Cov.: 31 AF XY: 0.782 AC XY: 58110 AN XY: 74294

African (AFR) AF: 0.420 AC: 17371 AN: 41372

American (AMR) AF: 0.865 AC: 13205 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3166 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4263 AN: 5160

South Asian (SAS) AF: 0.845 AC: 4069 AN: 4814

European-Finnish (FIN) AF: 0.962 AC: 10155 AN: 10554

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63102 AN: 68004

Other (OTH) AF: 0.796 AC: 1682 AN: 2112

Alfa AF: 0.868 Hom.: 180142

Bravo AF: 0.752

Asia WGS AF: 0.831 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.26
PhyloP100		-0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs974379; hg19: chr15-33505067;